BioMagResBank (BMRB) as a Resource for Structural Biology

Abstract

The Biological Magnetic Resonance Data Bank (BioMagResBank or BMRB), founded in 1988, serves as the archive for data generated by nuclear magnetic resonance (NMR) spectroscopy of biological systems. NMR spectroscopy is unique among biophysical approaches in its ability to provide a broad range of atomic and higher-level information relevant to the structural, dynamic, and chemical properties of biological macromolecules, as well as report on metabolite and natural product concentrations in complex mixtures and their chemical structures. BMRB became a core member of the Worldwide Protein Data Bank (wwPDB) in 2007, and the BMRB archive is now a core archive of the wwPDB. Currently, about 10% of the structures deposited into the PDB archive are based on NMR spectroscopy. BMRB stores experimental and derived data from biomolecular NMR studies. Newer BMRB biopolymer depositions are divided about evenly between those associated with structure determinations (atomic coordinates and supporting information archived in the PDB) and those reporting experimental information on molecular dynamics, conformational transitions, ligand binding, assigned chemical shifts, or other results from NMR spectroscopy. BMRB also provides resources for NMR studies of metabolites and other small molecules that are often macromolecular ligands and/or nonstandard residues. This chapter is directed to the structural biology community rather than the metabolomics and natural products community. Our goal is to describe various BMRB services offered to structural biology researchers and how they can be accessed and utilized. These services can be classified into four main groups: (1) data deposition, (2) data retrieval, (3) data analysis, and (4) services for NMR spectroscopists and software developers. The chapter also describes the NMR-STAR data format used by BMRB and the tools provided to facilitate its use. For programmers, BMRB offers an application programming interface (API) and libraries in the Python and R languages that enable users to develop their own BMRB-based tools for data analysis, visualization, and manipulation of NMR-STAR formatted files. BMRB also provides users with direct access tools through the NMRbox platform.

Keywords: Analysis; BMRB; BioMagResBank; Data formats; Deposition; NMR data; NMR spectra; NMR-STAR; PDB; Python; R; Retrieval; Search; Structures; Time-domain data; Visualization.

Fig. 1

NMR-STAR template generator initial interface

Fig. 2

NMR-STAR chemical shift assignment template generator interface

Fig. 3

BMRBdep interface for data files deposition

Fig. 4

The BMRBdep navigation menu

Fig. 5

The advanced search interface

Fig. 6

Search archive sub-menu in the navigation panel

Fig. 7

Main query grid page

Fig. 8

Listings obtain by selecting “DNA” and “¹H Chemical Shifts” on the main query grid page

Fig. 9

New query grid obtained by selecting “Proteins/Peptides” in the main query grid page

Fig. 10

NMR Restraints Grid interface

Fig. 11

The STARch file data converted interface

Fig. 12

Calculated CS-Rosetta structures for BMRB entry 19193

Fig. 13

The NMR-STAR viewer

Fig. 14

Chemical shift histogram for CB atoms in BMRB, generated using the PyBMRB library as explained in the text

Fig. 15

Interactive diagram showing the chemical shift correlation between CB and N atoms in cysteine across BMRB, generated using the PyBMRB library

Fig. 16

PyBMRB-generated simulated HSQC overlapping spectra comparing three BMRB entries

Fig. 17

This simulated HSQC overlapping spectrum comparing a user-uploaded spectrum with three similar entries in BMRB was generated using PyBMRB